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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Fredicting ligand-binding function in families of hacterial receptors
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Fredicting ligand-binding function in families of hacterial receptors

机译：细菌受体家族中配体结合功能的预测

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摘要

The three-dimensional fold of a new protein sequence can often be inferred directly from sequence homology to a protein of known structure. The function of a new protein sequence is more difficult to predict. however, since homologues can have different molec- ular and cellular functions. To develop and automate computa- tional methods for determining molecular function. we have an- alyzed ligand-binding specificity in two related families of binding proteins. One of these families includes Escherichia coli lactose repressor and ribose-binding protein. and the other includes E coli sulfate- and phosphate-binding proteins. These proteins have similar folds but varying specificity, binding many different small molecules, including mono- and disaccharides, purines. oxyanions. ferric iron, and polyamines. Starting from template structural alignments, alignments of over 90 sequences per family were generated by iterative database searches with hidden Markov models. Phylogenetic trees were made of full-length sequences and of subsets of residues lining the binding cleft. to determine whether subbranches of the trees correlate with ligand-binding preference. Automated analyses of residues in the binding pocket were also used to predict ligand-binding function for many un- characterized database sequences and to identify specific side chain-ligand contacts in proteins without solved structures. Our results demonstrate the utility of anchoring functional annotation within a protein family context.
机译：通常可以从序列同源性直接推断出具有已知结构的蛋白质，从而可以推断出新蛋白质序列的三维折叠。新蛋白质序列的功能更难预测。但是，由于同系物可以具有不同的分子和细胞功能。开发和自动化确定分子功能的计算方法。我们在两个相关的结合蛋白家族中分析了配体结合特异性。这些家族之一包括大肠杆菌乳糖阻遏蛋白和核糖结合蛋白。另一个包括大肠杆菌的硫酸盐和磷酸盐结合蛋白。这些蛋白质具有相似的折叠但具有不同的特异性，结合许多不同的小分子，包括单糖和二糖，嘌呤。氧阴离子。铁和多胺。从模板结构比对开始，通过使用隐马尔可夫模型进行的迭代数据库搜索，可以生成每个家族超过90个序列的比对。系统发育树由全长序列和结合裂隙衬里的残基子集组成。确定树木的亚支行是否与配体结合偏好相关。结合袋中残基的自动分析还用于预测许多未表征的数据库序列的配体结合功能，并鉴定蛋白质中没有溶解结构的特定侧链-配体接触。我们的结果证明了在蛋白质家族环境中锚定功能注释的效用。

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